Merge pull request #2787 from GEOS-ESM/develop

.circleci/config.yml

@@ -26,46 +26,20 @@ orbs:
 workflows:
  build-and-test-MAPL:
  jobs:
- # Builds MAPL in a "default" way - Intel
+ # Builds MAPL in a "default" way
  - ci/build:
  name: build-and-test-MAPL-on-<< matrix.compiler >>-using-<< matrix.cmake_generator >>
  context:
  - docker-hub-creds
  matrix:
  parameters:
- compiler: [ifort]
+ compiler: [gfortran,ifort]
  cmake_generator: ['Unix Makefiles','Ninja']
  baselibs_version: *baselibs_version
  repo: MAPL
  mepodevelop: false
  run_unit_tests: true
- ctest_options: "-LE 'PERFORMANCE|EXTDATA1G_BIG_TESTS|EXTDATA2G_BIG_TESTS' --output-on-failure"
- persist_workspace: true # Needed for MAPL tutorials
-
- # Builds MAPL in a "default" way - GNU
- #
- # NOTE: Currently Open MPI fails on the bundleio with:
- #
- # The OSC pt2pt component does not support MPI_THREAD_MULTIPLE in this release.
- # Workarounds are to run on a single node, or to use a system with an RDMA
- # capable network such as Infiniband.
- #
- # For now, we run GNU/Open MPI without the bundleio tests. Some indications that
- # Open MPI 5 will not have this limitation
-
- - ci/build:
- name: build-and-test-MAPL-on-<< matrix.compiler >>-using-<< matrix.cmake_generator >>
- context:
- - docker-hub-creds
- matrix:
- parameters:
- compiler: [gfortran]
- cmake_generator: ['Unix Makefiles','Ninja']
- baselibs_version: *baselibs_version
- repo: MAPL
- mepodevelop: false
- run_unit_tests: true
- ctest_options: "-E bundleio -LE 'PERFORMANCE|EXTDATA1G_BIG_TESTS|EXTDATA2G_BIG_TESTS' --output-on-failure"
+ ctest_options: "-L 'ESSENTIAL' --output-on-failure"
  persist_workspace: true # Needed for MAPL tutorials
 
  # Builds MAPL like UFS does (no FLAP and pFlogger, static)
@@ -83,7 +57,7 @@ workflows:
  remove_pflogger: true
  extra_cmake_options: "-DBUILD_WITH_FLAP=OFF -DBUILD_WITH_PFLOGGER=OFF -DBUILD_WITH_FARGPARSE=OFF -DUSE_EXTDATA2G=OFF -DBUILD_SHARED_MAPL=OFF"
  run_unit_tests: true
- ctest_options: "-LE 'PERFORMANCE|EXTDATA1G_BIG_TESTS|EXTDATA2G_BIG_TESTS' --output-on-failure"
+ ctest_options: "-L 'ESSENTIAL' --output-on-failure"
 
  # Run MAPL Tutorials
  - ci/run_mapl_tutorial:
@@ -92,8 +66,7 @@ workflows:
  - docker-hub-creds
  matrix:
  parameters:
- #compiler: [gfortran, ifort]
- compiler: [ifort]
+ compiler: [gfortran, ifort]
  tutorial_name:
  - hello_world
  - parent_no_children
@@ -108,29 +81,14 @@ workflows:
 
  build-and-run-GEOSgcm:
  jobs:
- # Build GEOSgcm -- ifort
- - ci/build:
- name: build-GEOSgcm-on-<< matrix.compiler >>
- context:
- - docker-hub-creds
- matrix:
- parameters:
- compiler: [ifort]
- baselibs_version: *baselibs_version
- repo: GEOSgcm
- checkout_fixture: true
- mepodevelop: true
- checkout_mapl_branch: true
- persist_workspace: true # Needs to be true to run fv3/gcm experiment, costs extra, retained for one day
-
- # Build GEOSgcm -- GCC
+ # Build GEOSgcm
  - ci/build:
  name: build-GEOSgcm-on-<< matrix.compiler >>
  context:
  - docker-hub-creds
  matrix:
  parameters:
- compiler: [gfortran]
+ compiler: [gfortran, ifort]
  baselibs_version: *baselibs_version
  repo: GEOSgcm
  checkout_fixture: true
@@ -170,29 +128,14 @@ workflows:
 
  build-GEOSldas:
  jobs:
- # Build GEOSldas on ifort
- - ci/build:
- name: build-GEOSldas-on-<< matrix.compiler >>
- context:
- - docker-hub-creds
- matrix:
- parameters:
- compiler: [ifort]
- baselibs_version: *baselibs_version
- repo: GEOSldas
- mepodevelop: false
- checkout_fixture: true
- fixture_branch: develop
- checkout_mapl_branch: true
-
- # Build GEOSldas on gfortran
+ # Build GEOSldas
  - ci/build:
  name: build-GEOSldas-on-<< matrix.compiler >>
  context:
  - docker-hub-creds
  matrix:
  parameters:
- compiler: [gfortran]
+ compiler: [gfortran,ifort]
  baselibs_version: *baselibs_version
  repo: GEOSldas
  mepodevelop: false

.github/actions/deploy-ford-docs/action.yml

@@ -61,12 +61,14 @@ runs:
  shell: bash
 
  - name: Build Documentation
- run: ford ${{ inputs.ford-input }}
+ run: |
+ cd docs/Ford
+ ford ${{ inputs.ford-input }}
  shell: bash
 
  - name: Deploy Pages
  uses: JamesIves/github-pages-deploy-action@v4
- if: github.event_name == 'push' && github.repository == 'GEOS-ESM/MAPL' && ( startsWith( github.ref, 'refs/tags/v' ) || github.ref == 'refs/heads/main' )
+ if: github.event_name == 'push' && github.repository == 'GEOS-ESM/MAPL' && ( startsWith( github.ref, 'refs/tags/v' ) || github.ref == 'refs/heads/main' || github.ref == 'refs/heads/release/MAPL-v3' )
  with:
  folder: ${{ inputs.doc-folder }}
  token: ${{ inputs.token }}

.github/workflows/docs.yml

@@ -21,7 +21,11 @@ jobs:
  - name: Build and Deploy Docs
  uses: ./.github/actions/deploy-ford-docs
  with:
- ford-input: docs/Ford/docs-with-remote-esmf.md
+ # Due to a bug in ford, for now we do *not* want to use
+ # the full path to the ford input file. Rather, the
+ # action will cd into docs/Ford and then run ford
+ # relative path to the ford input file.
+ ford-input: docs-with-remote-esmf.md
  doc-folder: docs/Ford/doc
  token: ${{ secrets.GITHUB_TOKEN }}
 
@@ -34,7 +38,11 @@ jobs:
  - name: Build and Deploy Dev Docs
  uses: ./.github/actions/deploy-ford-docs
  with:
- ford-input: docs/Ford/docs-with-remote-esmf.public_private_protected.md
+ # Due to a bug in ford, for now we do *not* want to use
+ # the full path to the ford input file. Rather, the
+ # action will cd into docs/Ford and then run ford
+ # relative path to the ford input file.
+ ford-input: docs-with-remote-esmf.public_private_protected.md
  doc-folder: docs/Ford/dev-doc
  token: ${{ secrets.GITHUB_TOKEN }}
  target-folder: dev-doc

.github/workflows/trigger-circleci-pipeline-on-release.yml

@@ -7,6 +7,6 @@ jobs:
  steps:
  - name: CircleCI Trigger on Release
  id: docker-build
- uses: CircleCI-Public/trigger-circleci-pipeline-action@v1.1.0
+ uses: CircleCI-Public/trigger-circleci-pipeline-action@v1.2.0
  env:
  CCI_TOKEN: ${{ secrets.CCI_TOKEN }}

.github/workflows/workflow.yml

@@ -13,11 +13,29 @@ on:
  - ".editorconfig"
 
 jobs:
+ check-ford-docs:
+ name: Build Ford Docs
+ runs-on: ubuntu-latest
+ steps:
+ - name: Checkout
+ uses: actions/checkout@v4
+
+ - name: Build and Deploy Docs
+ uses: ./.github/actions/deploy-ford-docs
+ with:
+ # Due to a bug in ford, for now we do *not* want to use
+ # the full path to the ford input file. Rather, the
+ # action will cd into docs/Ford and then run ford
+ # relative path to the ford input file.
+ ford-input: ford-ci.md
+ doc-folder: docs/Ford/ci-doc
+ token: ${{ secrets.GITHUB_TOKEN }}
+
  build_test_mapl:
  name: Build and Test MAPL GNU
  runs-on: ubuntu-latest
  container:
- image: gmao/ubuntu20-geos-env-mkl:v7.23.0-openmpi_5.0.0-gcc_12.1.0
+ image: gmao/ubuntu20-geos-env-mkl:v7.23.0-openmpi_5.0.2-gcc_13.2.0
  # Per https://github.com/actions/virtual-environments/issues/1445#issuecomment-713861495
  # It seems like we might not need secrets on GitHub Actions which is good for forked
  # pull requests
@@ -63,16 +81,7 @@ jobs:
  run: |
  cd build
  make -j4 build-tests
- # skip performance tests
- # NOTE: Currently Open MPI fails on the bundleio with:
- #
- # The OSC pt2pt component does not support MPI_THREAD_MULTIPLE in this release.
- # Workarounds are to run on a single node, or to use a system with an RDMA
- # capable network such as Infiniband.
- #
- # For now, we run GNU/Open MPI without the bundleio tests. Some indications that
- # Open MPI 5 will not have this limitation
- ctest -E bundleio -LE 'PERFORMANCE|EXTDATA1G_BIG_TESTS|EXTDATA2G_BIG_TESTS' --output-on-failure
+ ctest -L 'ESSENTIAL' --output-on-failure
  build_test_mapl_intel:
  name: Build and Test MAPL Intel
  runs-on: ubuntu-latest
@@ -119,5 +128,4 @@ jobs:
  run: |
  cd build
  make -j4 build-tests
- # skip performance tests
- ctest -LE 'PERFORMANCE|EXTDATA1G_BIG_TESTS|EXTDATA2G_BIG_TESTS' --output-on-failure
+ ctest -L 'ESSENTIAL' --output-on-failure

Apps/CMakeLists.txt

@@ -10,6 +10,8 @@ file (COPY mapl_stub.pl DESTINATION ${esma_etc}/MAPL)
 
 install (PROGRAMS
  MAPL_GridCompSpecs_ACG.py
+ combine_restarts.py
+ split_restart.py
  mapl_acg.pl
  mapl_stub.pl
  TYPE SYSCONF

Apps/MAPL_GridCompSpecs_ACG.py

@@ -28,6 +28,26 @@
 string_emit = lambda value: ("'" + value + "'") if value else None
 # Return value in brackets
 array_emit = lambda value: ('[' + value + ']') if value else None
+lstripped = lambda s: s.lower().strip(' .')
+
+# emit function for character arrays
+string_array_emit = lambda value: make_string_array(value) if value else None
+
+def make_string_array(s):
+ """ Returns a string representing a Fortran character array """
+ ss = s.strip()
+ if ',' in ss:
+ ls = [s.strip() for s in s.strip().split(',')]
+ else:
+ ls = s.strip().split()
+ ls = [rm_quotes(s) for s in ls]
+ ls = [s for s in ls if s]
+ n = max(ls)
+ ss = ','.join([add_quotes(s) for s in ls])
+ return f"[character(len={n}) :: {ss}]"
+
+rm_quotes = lambda s: s.strip().strip('"\'').strip()
+add_quotes = lambda s: "'" + s + "'"
 
 mangle_name = lambda name: string_emit(name.replace("*","'//trim(comp_name)//'")) if name else None 
 make_internal_name = lambda name: name.replace('*','') if name else None
@@ -49,6 +69,12 @@ def make_entry_emit(dictionary):
  'REQ' : 'MAPL_RestartRequired', 'BOOT' : 'MAPL_RestartBoot',
  'SKIPI': 'MAPL_RestartSkipInitial'})
 
+# emit function for logical-valued options
+TRUEVALUES = {'t', 'true', 'yes', 'y', 'si', 'oui', 'sim'}
+FALSEVALUES = {'f', 'false', 'no', 'n', 'no', 'non', 'nao'}
+TRUE_VALUE = '.true.'
+FALSE_VALUE = '.false.'
+logical_emit = lambda s: TRUE_VALUE if lstripped(s) in TRUEVALUES else FALSE_VALUE if lstripped(s) in FALSEVALUES else None
 # emit function for Option.ADD2EXPORT
 ADD2EXPORT_EMIT = make_entry_emit({'T': '.true.', 'F': '.false.'})
 
@@ -89,6 +115,8 @@ def get_mandatory_options(cls):
  'AVINT': ('averaging_interval',),
  'DATATYPE': ('datatype',),
  'DEFAULT': ('default',),
+ 'DEPENDS_ON_CHILDREN': ('depends_on_children', logical_emit),
+ 'DEPENDS_ON': ('depends_on', string_array_emit),
  'FIELD_TYPE': ('field_type',),
  'FRIENDLYTO': ('friendlyto', string_emit),
  'FRIEND2': ('friendlyto', string_emit),

Apps/Regrid_Util.F90

@@ -557,8 +557,8 @@ subroutine generate_report()
  call reporter%add_column(FormattedTextColumn('% Excl','(f6.2)', 6, PercentageColumn(ExclusiveColumn('MEAN'))))
  call reporter%add_column(FormattedTextColumn(' Max Excl)','(f9.6)', 9, ExclusiveColumn('MAX')))
  call reporter%add_column(FormattedTextColumn(' Min Excl)','(f9.6)', 9, ExclusiveColumn('MIN')))
- call reporter%add_column(FormattedTextColumn('Max PE)','(1x,i4.4,1x)', 6, ExclusiveColumn('MAX_PE')))
- call reporter%add_column(FormattedTextColumn('Min PE)','(1x,i4.4,1x)', 6, ExclusiveColumn('MIN_PE')))
+ call reporter%add_column(FormattedTextColumn('Max PE)','(1x,i5.5,1x)', 7, ExclusiveColumn('MAX_PE')))
+ call reporter%add_column(FormattedTextColumn('Min PE)','(1x,i5.5,1x)', 7, ExclusiveColumn('MIN_PE')))
  report_lines = reporter%generate_report(t_prof)
  if (mapl_am_I_root()) then
  write(*,'(a)')'Final profile'